# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters using config directory /augustus/config/ ...
# Using protein profile unknown
# --[4..37]--> unknown_A (12) <--[0..9]--> unknown_B (24) <--[0..1]--> unknown_C (20) <--[0..3]--> unknown_D (107) <--[0..1]--> unknown_E (52) <--[0..34]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig11689020180911_busco_2432604931_.temp is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 2409, name = Contig116890) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig116890	AUGUSTUS	gene	1045	1527	0.49	+	.	g1
Contig116890	AUGUSTUS	transcript	1045	1527	0.49	+	.	g1.t1
Contig116890	AUGUSTUS	start_codon	1045	1047	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig116890	AUGUSTUS	CDS	1045	1527	0.49	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig116890	AUGUSTUS	stop_codon	1525	1527	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggaaattgtgacccttatttctatattaacaggaattgcttctgatggcctgaaggggcgtgtgtttgaagtctccc
# tggctgaccttcagaatgatgaggtgtccttcaggaagtttaaactgatggctgaggaagttcaaggtcgtaacgtcctgaccaacttccacggtatg
# gacctgaccagggacaagctctgctccatggtgaagaaatggcagaccctgatccaggctcatgttgatgttaagactacagatggctaccttctgag
# aatgttctgtattggttttaccaagaagaagcagtttcaagtgaagaaaacttgttatgcccagcacacacaggtaggaaatcagatggaaaatttgt
# tttatgatgtacaaatcttctatgcccaaaatattcaaatcacccctgaattagaaagcttgggccgatatagtattgcgttaggtgatgacactgtc
# gaatctgtttga]
# protein sequence = [MEIVTLISILTGIASDGLKGRVFEVSLADLQNDEVSFRKFKLMAEEVQGRNVLTNFHGMDLTRDKLCSMVKKWQTLIQ
# AHVDVKTTDGYLLRMFCIGFTKKKQFQVKKTCYAQHTQVGNQMENLFYDVQIFYAQNIQITPELESLGRYSIALGDDTVESV]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370PBD.prfl --predictionStart=0  --predictionEnd=21395  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig11689020180911_busco_2432604931_.temp